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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 | DESeq Differential expression analysis based on the
Negative Binomial (a.k.a. Gamma-Poisson)
distribution
DESeq2-package DESeq2 package for differential analysis of
count data
DESeqDataSet-class DESeqDataSet object and constructors
DESeqResults-class DESeqResults object and constructor
DESeqTransform-class DESeqTransform object and constructor
coef Extract a matrix of model coefficients/standard
errors
collapseReplicates Collapse technical replicates in a
RangedSummarizedExperiment or DESeqDataSet
counts Accessors for the 'counts' slot of a
DESeqDataSet object.
design Accessors for the 'design' slot of a
DESeqDataSet object.
dispersionFunction Accessors for the 'dispersionFunction' slot of
a DESeqDataSet object.
dispersions Accessor functions for the dispersion estimates
in a DESeqDataSet object.
estimateBetaPriorVar Steps for estimating the beta prior variance
estimateDispersions Estimate the dispersions for a DESeqDataSet
estimateDispersionsGeneEst
Low-level functions to fit dispersion estimates
estimateSizeFactors Estimate the size factors for a 'DESeqDataSet'
estimateSizeFactorsForMatrix
Low-level function to estimate size factors
with robust regression.
fpkm FPKM: fragments per kilobase per million mapped
fragments
fpm FPM: fragments per million mapped fragments
lfcShrink Shrink log2 fold changes
makeExampleDESeqDataSet
Make a simulated DESeqDataSet
nbinomLRT Likelihood ratio test (chi-squared test) for
GLMs
nbinomWaldTest Wald test for the GLM coefficients
normTransform Normalized counts transformation
normalizationFactors Accessor functions for the normalization
factors in a DESeqDataSet object.
normalizeGeneLength Normalize for gene length
plotCounts Plot of normalized counts for a single gene
plotDispEsts Plot dispersion estimates
plotMA MA-plot from base means and log fold changes
plotPCA Sample PCA plot for transformed data
plotSparsity Sparsity plot
priorInfo Accessors for the 'priorInfo' slot of a
DESeqResults object.
replaceOutliers Replace outliers with trimmed mean
results Extract results from a DESeq analysis
rlog Apply a 'regularized log' transformation
show Show method for DESeqResults objects
sizeFactors Accessor functions for the 'sizeFactors'
information in a DESeqDataSet object.
summary Summarize DESeq results
unmix Unmix samples using loss in a variance
stabilized space
varianceStabilizingTransformation
Apply a variance stabilizing transformation
(VST) to the count data
vst Quickly estimate dispersion trend and apply a
variance stabilizing transformation
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